LAMMPS (13 Oct 2016)
# sample LAMMPS input script for thermal conductivity of liquid LJ
# Green-Kubo method via compute heat/flux and fix ave/correlate

# settings

variable	x equal 10
variable	y equal 10
variable	z equal 10

variable	rho equal 0.6
variable        t equal 1.35
variable	rc equal 2.5

#variable	rho equal 0.85
#variable        t equal 0.7
#variable	rc equal 3.0

variable    p equal 200     # correlation length
variable    s equal 10      # sample interval
variable    d equal $p*$s   # dump interval
variable    d equal 200*$s   
variable    d equal 200*10   

# setup problem

units		lj
atom_style	atomic

lattice		fcc ${rho}
lattice		fcc 0.6
Lattice spacing in x,y,z = 1.88207 1.88207 1.88207
region		box block 0 $x 0 $y 0 $z
region		box block 0 10 0 $y 0 $z
region		box block 0 10 0 10 0 $z
region		box block 0 10 0 10 0 10
create_box	1 box
Created orthogonal box = (0 0 0) to (18.8207 18.8207 18.8207)
  2 by 2 by 2 MPI processor grid
create_atoms	1 box
Created 4000 atoms
mass		1 1.0

velocity	all create $t 87287
velocity	all create 1.35 87287

pair_style	lj/cut ${rc}
pair_style	lj/cut 2.5
pair_coeff	1 1 1.0 1.0

neighbor	0.3 bin
neigh_modify	delay 0 every 1

# 1st equilibration run

fix		1 all nvt temp $t $t 0.5
fix		1 all nvt temp 1.35 $t 0.5
fix		1 all nvt temp 1.35 1.35 0.5
thermo		100
run		1000
Neighbor list info ...
  1 neighbor list requests
  update every 1 steps, delay 0 steps, check yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 2.8
  ghost atom cutoff = 2.8
  binsize = 1.4 -> bins = 14 14 14
Memory usage per processor = 2.52285 Mbytes
Step Temp E_pair E_mol TotEng Press 
       0         1.35   -4.1241917            0   -2.0996979   -3.1962625 
     100    1.1997886   -3.7796264            0   -1.9803934    0.4889458 
     200     1.271238   -3.7354981            0   -1.8291178    0.6873844 
     300    1.3346808   -3.6942841            0   -1.6927634   0.84332881 
     400    1.4020848   -3.7118654            0   -1.6092641   0.87670585 
     500    1.3723622   -3.6917931            0   -1.6337644   0.92172921 
     600    1.3451676   -3.7281573            0   -1.7109103   0.76029091 
     700    1.3021567   -3.6876155            0   -1.7348687   0.82721085 
     800    1.3489121   -3.7082852            0   -1.6854229   0.86438061 
     900    1.3708803   -3.6966168            0   -1.6408103     0.921415 
    1000    1.3640742   -3.7075319            0   -1.6619322   0.86651332 
Loop time of 0.457959 on 8 procs for 1000 steps with 4000 atoms

Performance: 943316.262 tau/day, 2183.602 timesteps/s
98.9% CPU use with 8 MPI tasks x no OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.23307    | 0.24263    | 0.2466     |   1.0 | 52.98
Neigh   | 0.10661    | 0.11011    | 0.11166    |   0.5 | 24.04
Comm    | 0.069595   | 0.075354   | 0.087444   |   2.2 | 16.45
Output  | 0.00028014 | 0.00028831 | 0.00031686 |   0.1 |  0.06
Modify  | 0.01694    | 0.01904    | 0.021602   |   1.2 |  4.16
Other   |            | 0.01053    |            |       |  2.30

Nlocal:    500 ave 510 max 479 min
Histogram: 1 0 0 0 0 2 1 1 0 3
Nghost:    1519 ave 1539 max 1509 min
Histogram: 2 0 4 0 0 0 0 1 0 1
Neighs:    13553.8 ave 14051 max 12567 min
Histogram: 1 0 0 0 1 0 2 1 1 2

Total # of neighbors = 108430
Ave neighs/atom = 27.1075
Neighbor list builds = 155
Dangerous builds = 0

velocity	all scale $t
velocity	all scale 1.35

unfix		1

# thermal conductivity calculation

reset_timestep  0

compute         myKE all ke/atom
compute         myPE all pe/atom
compute         myStress all stress/atom NULL virial
compute         flux all heat/flux myKE myPE myStress
variable        Jx equal c_flux[1]/vol
variable        Jy equal c_flux[2]/vol
variable        Jz equal c_flux[3]/vol

fix	        1 all nve
fix             JJ all ave/correlate $s $p $d                 c_flux[1] c_flux[2] c_flux[3] type auto 	        file profile.heatflux ave running
fix             JJ all ave/correlate 10 $p $d                 c_flux[1] c_flux[2] c_flux[3] type auto 	        file profile.heatflux ave running
fix             JJ all ave/correlate 10 200 $d                 c_flux[1] c_flux[2] c_flux[3] type auto 	        file profile.heatflux ave running
fix             JJ all ave/correlate 10 200 2000                 c_flux[1] c_flux[2] c_flux[3] type auto 	        file profile.heatflux ave running

variable        scale equal $s*dt/$t/$t/vol
variable        scale equal 10*dt/$t/$t/vol
variable        scale equal 10*dt/1.35/$t/vol
variable        scale equal 10*dt/1.35/1.35/vol
variable        k11 equal trap(f_JJ[3])*${scale}
variable        k11 equal trap(f_JJ[3])*4.11522633744856e-06
variable        k22 equal trap(f_JJ[4])*${scale}
variable        k22 equal trap(f_JJ[4])*4.11522633744856e-06
variable        k33 equal trap(f_JJ[5])*${scale}
variable        k33 equal trap(f_JJ[5])*4.11522633744856e-06

thermo	        $d
thermo	        2000
thermo_style    custom step temp v_Jx v_Jy v_Jz v_k11 v_k22 v_k33

run             100000
Memory usage per processor = 4.39785 Mbytes
Step Temp v_Jx v_Jy v_Jz v_k11 v_k22 v_k33 
       0         1.35  0.012561273 -0.087295611 -0.037041124  0.014429409   0.69689289   0.12547278 
    2000    1.3455113 -0.034571206  -0.17570902 -0.057218308   -1.6110148    7.9287556    8.5035767 
    4000    1.3477761 -0.029528723  0.018790489  0.056107464     7.698411    1.9459053    9.9605272 
    6000    1.3411436  -0.20281149    0.2184806  0.036024028    4.6533075    1.6223216    3.7246529 
    8000    1.3561682   0.12038719  0.034930957   0.12173601    4.6450263    1.9032849    2.7566363 
   10000    1.3397694  -0.14241489  -0.10956496  0.053088086    6.4191535    3.1582257    2.2786677 
   12000    1.3410756 0.0033462395   0.14337321   0.16381733    5.9663779    1.6774436    1.7442075 
   14000    1.3484928 0.0080419803 -0.080232102  0.039035519    4.9483626    1.6210893    1.6103343 
   16000    1.3414836  -0.11063045 -0.031557643  0.032060333    6.1381241     1.438198    1.5831541 
   18000    1.3488617   0.15908507 -0.021418806  -0.13992507    5.9198613    1.1016464    1.2905478 
   20000    1.3535727   0.13217689  0.071933521 -0.028452943    6.3746606     1.003194    1.7007101 
   22000    1.3408534 -0.078953557 -0.0022323663  -0.22979033    5.0105241    1.1489328     1.720847 
   24000      1.34722  0.074784199 -0.071218632   0.15238165    4.4835452   0.94086945    3.1603615 
   26000    1.3539218  0.052534363   0.10419096    0.1866213    4.2233104    1.3973253    3.2802881 
   28000    1.3510105 0.0080425673  -0.03723976   0.20758595     5.261917    1.1931088     3.498831 
   30000    1.3410807 -0.043957884  0.065683978  0.015386362    4.3815277    1.5000017    3.2237565 
   32000      1.34766 -0.060481287   0.17142383  0.034367135    4.0974942    1.1637027    3.3771953 
   34000    1.3417583  -0.10055844  0.050237668   0.06974988    4.1478021    1.0235517    2.9440249 
   36000    1.3468728   0.09375756  -0.17875264 -0.063513807    4.4412987   0.71084371    3.4316313 
   38000    1.3496868 -0.038635804     0.117965  0.018050271     4.962332   0.41701129    3.4690212 
   40000    1.3403452 -0.092158116   0.14432655 -0.062258229    4.9980486    0.3762815    3.1688552 
   42000    1.3498661  0.085807945  0.010256385 -0.002956898    4.8200626   0.29278287     3.094633 
   44000    1.3564084  -0.07415163 -0.051327929  -0.18457986    4.7070907    0.3358167    3.0741797 
   46000    1.3435866 -0.013911463  0.081813372  0.022628846    4.6043718    0.3682401    2.9956189 
   48000     1.350611  0.036512747  0.080481423  -0.22973181    4.5648715   0.32728516    3.8573343 
   50000    1.3421783  0.057665789  0.075597141   0.17377918    4.4278473    0.5383886    3.5866168 
   52000    1.3473497  -0.11159587  -0.09688769   0.19876168    4.3876613   0.43408155    3.4786305 
   54000    1.3459495  -0.15341705  0.063996148 -0.0038254597    4.8434026   0.62047297     3.445187 
   56000    1.3545654 -0.082406034  0.089232864 -0.024355614     4.546051    0.7367607    3.3694561 
   58000    1.3577504  0.082844384  0.019500036  0.073721698    4.4061886    1.4575694    3.2754066 
   60000     1.348614  -0.16190321 -0.048576343  0.093820555    4.2946463    1.3416919    3.1159234 
   62000    1.3551143  0.097443296  -0.04420265  -0.25713945    4.1260882    1.2550603     3.063215 
   64000     1.346239  0.019198575 -0.095746619   0.18383922    4.5691519    1.2615165    2.9935539 
   66000    1.3535383 -0.0035547901   -0.1753318  0.014025292    4.5371394    1.0740671    2.9362916 
   68000    1.3421249  -0.18217113  0.077901408   0.04314081    5.1644747    1.0218342    2.9789097 
   70000    1.3446114  0.029565781  -0.13771336  0.050328878    5.4811405    1.0430806    2.9748623 
   72000    1.3692655  0.005711741   0.13966773 -0.062638787    5.3033385    1.1040582    2.7599218 
   74000    1.3405365 -0.054281977  0.038019086 -0.024980877    5.1246258    2.0782965     2.725331 
   76000    1.3644178  0.040847675 -0.051968108  -0.12259032    5.1218657    1.8504273    2.6804003 
   78000     1.353792 -0.093663092  0.018784967 -0.073871437     5.025196    1.7789709    2.5339006 
   80000    1.3520982  -0.09407101  0.010328039 0.0028841073    5.1410049     1.855057    2.6935895 
   82000    1.3447597  -0.11935066   -0.2184608  0.073543056    5.2645334    1.7883077    4.2012292 
   84000    1.3712151 -0.064367612  0.021246872 -0.033571866    5.0479674    1.8947341    4.3856536 
   86000    1.3453867 -0.029842112 -0.042297039   0.05422886    5.0667777    2.0365983    4.4542311 
   88000    1.3439543  -0.21625828 -0.028119372 -0.010320332    4.9946428    2.3095763    4.3429587 
   90000    1.3472579  0.058391002  0.037139373   0.03424008    5.0599004    2.8132794    4.4503426 
   92000     1.361788  0.028891114  0.072799744  -0.12035229    4.8759851    2.5130025    4.2747068 
   94000    1.3440566  0.043421348  0.049653856 -0.060444094    4.8884081    2.5072981    4.3105221 
   96000    1.3537566  0.088733517  -0.11449828 -0.049852036    4.8115085    2.4780963    4.2213579 
   98000    1.3373399   0.25457663 -0.041723778 0.00084565184    4.7163394    2.4100822     4.485536 
  100000    1.3487502  0.046333889    0.1247351  0.063467467    4.6563279    2.4049358    4.5742925 
Loop time of 49.532 on 8 procs for 100000 steps with 4000 atoms

Performance: 872163.631 tau/day, 2018.897 timesteps/s
99.6% CPU use with 8 MPI tasks x no OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 27.027     | 27.478     | 28.167     |   6.9 | 55.48
Neigh   | 11.257     | 11.369     | 11.491     |   2.3 | 22.95
Comm    | 6.6783     | 7.6942     | 8.2758     |  19.3 | 15.53
Output  | 0.0075166  | 0.024356   | 0.026799   |   4.1 |  0.05
Modify  | 1.7374     | 1.7617     | 1.7845     |   1.0 |  3.56
Other   |            | 1.205      |            |       |  2.43

Nlocal:    500 ave 505 max 491 min
Histogram: 1 0 0 1 0 1 0 2 2 1
Nghost:    1529.88 ave 1548 max 1508 min
Histogram: 1 1 0 0 1 1 2 0 0 2
Neighs:    13569.8 ave 13906 max 13235 min
Histogram: 1 1 0 1 1 1 1 1 0 1

Total # of neighbors = 108558
Ave neighs/atom = 27.1395
Neighbor list builds = 16041
Dangerous builds = 0

variable        kappa equal (v_k11+v_k22+v_k33)/3.0
print           "running average conductivity: ${kappa}"
running average conductivity: 3.8785187495769
Total wall time: 0:00:50
